Ionisation of Atoms Determined by Kappa Refinement against 3D Electron Diffraction Data

The following submission contains the data reduction and processing files, dynamical refinement files, refinement files for theoretical structure factors, and CIF files of five inorganic compounds: quartz, natrolite, borane, caesium lead bromide, and lutetium aluminium garnet collected by 3D electron diffraction (3D ED) for studying ionisation of atoms by kappa refinement against 3D ED data.

The data set for quartz was collected using the precession-assisted 3D ED method and for borane, caesium lead bromide, and lutetium aluminium garnet was collected using the continuous-rotation 3D ED method. Two data sets were collected from the same crystal for natrolite using continuous-rotation and precession-assisted 3D ED method. The data reduction and processing were done using PETS2 (1) software and the dynamical refinements were performed using the JANA2020 (2) software. The refinements were performed in two primary stages: IAM refinements (without taking into consideration the effects of charge transfer between the atoms) and kappa refinements (by taking into consideration the effects of charge transfer between the atoms).

The submission also contains JANA2020 files of refinements against theoretical structure factors obtained using periodic DFT calculations and on the structure model obtained after IAM refinements of each of the experimental data sets.

The folders are divided according to the compounds. Each folder contains the relevant data reduction and processing files (PETS2 files), dynamical refinement files (JANA2020 files for IAM and kappa refinements), refinement files for theoretical structure factors (JANA2020 files for IAM and kappa refinements) and final CIF files (for IAM and kappa refinements).

References

1.         L. Palatinus, P. Brázda, M. Jelínek, J. Hrdá, G. Steciuk, M. Klementová, Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0. Acta Cryst B 75, 512–522 (2019).

2.         V. Petříček, L. Palatinus, J. Plášil, M. Dušek, Jana2020 – a new version of the crystallographic computing system Jana. Zeitschrift für Kristallographie - Crystalline Materials 238, 271–282 (2023).

The following table summarises the crystallographic information and data collection parameters for the data sets.

Crystal data

Sample

Quartz

Natrolite

Natrolite

Borane

Caesium lead bromide

Lutetium Aluminium Garnet

Chemical formula

SiO2

Na2Al2Si3O12H4

Na2Al2Si3O12H4

B18H22

CsPbBr3

Lu3Al5O12

Mr

60.1

380.2

380.2

108.4

579.8

851.8

Crystal system, space group

Trigonal, P3221

Orthorhombic, Fdd2

Orthorhombic, Fdd2

Orthorhombic, Pccn

Orthorhombic, Pbnm

Cubic, Ia3 ̅d

a, b, c (Å)

4.9012(24), 4.9012, 5.4068(26)

18.3885(1), 18.7183(32), 6.6569(11)

18.4125(9), 18.7073(7), 6.6306(2)

10.7789(17), 11.9869(16), 10.7338(17)

8.1189(4), 8.359(4), 11.7593(5)

11.9105(4), 11.9105(4), 11.9105(4)

α, β, γ (°)

90, 90, 120

90, 90, 90

90, 90, 90

90, 90, 90

90, 90, 90

90, 90, 90

V (Å3)

112.48(8)

2291.31(54)

2283.90(16)

1386.87(36)

798.1(1)

1689.6(1)

Z

3

8

8

4

4

8

Crystal size (mm)

0.0004

0.0005

0.0005

0.0015

0.0004

0.0003

Data collection

Diffractometer

TEM FEI Technei G2 20

TEM FEI Technei G2 20

TEM FEI Technei G2 20

TEM FEI Technei G2 20

TEM FEI Technei G2 20

TEM FEI Technei G2 20

3D ED method

Precession

Precession

Continuous Rotation

Continuous Rotation

Continuous Rotation

Continuous Rotation

Detector

Medipix 3 ASI Cheetah

Medipix 3 ASI Cheetah

Medipix 3 ASI Cheetah

Medipix 3 ASI Cheetah

Medipix 3 ASI Cheetah

Medipix 3 ASI Cheetah

Radiation source

LaB6

LaB6

LaB6

LaB6

LaB6

LaB6

Radiation type

Electron, λ = 0.0251 Å

Electron, λ = 0.0251 Å

Electron, λ = 0.0251 Å

Electron, λ = 0.0251 Å

Electron, λ = 0.0251 Å

Electron, λ = 0.0251 Å

Temperature (K)

293

95

95

100

153

153

(sin θ/λ)max (Å−1)

1.25

1.1

1.00

0.85

1.00

1.4

No. of measured, independent andobserved [I > 3σ(I)] reflections

3631, 1076, 1004 

15767, 6018, 4419 

12368, 4546, 4422 

30304, 13809, 4779

16736, 422, 363

23256, 1562, 1363

Software used

Data collection

RATS software

RATS software

RATS software

RATS software

RATS software

RATS software

Data reduction and processing

PETS2

PETS2

PETS2

PETS2

PETS2

PETS2

Refinement

JANA2020

JANA2020

JANA2020

JANA2020

JANA2020

JANA2020

DFT calculation

WIEN2k and Crystal23

WIEN2k

Crystal23

Crystal23

WIEN2k

WIEN2k